EHV-1 Canonic Transcript dynamics (TSS ~ TES)
Balázs Kakuk
## Error in read.table(file = file, header = header, sep = sep, quote = quote, :
## object 'config' not foundProject info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
Canonic Transcript dynamics (TSS ~ TES)
Those reads were counted only, where both the 3-prime AND the 5-prime adapters were “correct” (according to LoRTIA)
When counting with either adapters, the clustering grouped ORF64 together with two late genes
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.5)... Done.## Bootstrap (r = 0.59)... Done.## Bootstrap (r = 0.7)... Done.## Bootstrap (r = 0.79)... Done.## Bootstrap (r = 0.89)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.09)... Done.## Bootstrap (r = 1.2)... Done.## Bootstrap (r = 1.29)... Done.## Bootstrap (r = 1.39)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.5)... Done.## Bootstrap (r = 0.58)... Done.## Bootstrap (r = 0.69)... Done.## Bootstrap (r = 0.77)... Done.## Bootstrap (r = 0.88)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.08)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.27)... Done.## Bootstrap (r = 1.38)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 2: 1 ORF2 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 3: 1 ORF3 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 4: 1 ORF4 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 5: 1 ORF8 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 6: 1 ORF9 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 7: 1 ORF11 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 8: 1 ORF14 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 9: 1 ORF18 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 10: 1 ORF19 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 11: 1 ORF20 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 12: 1 ORF21 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 13: 1 ORF22 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 14: 1 ORF23 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 15: 1 ORF24 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 16: 1 ORF25 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 17: 1 ORF26 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 18: 1 ORF28 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 19: 1 ORF29 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 20: 1 ORF31 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 21: 1 ORF33 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 22: 1 ORF34 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 23: 1 ORF35.5 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 24: 1 ORF36 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 25: 1 ORF37 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 26: 1 ORF38 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 27: 1 ORF39 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 28: 1 CTO 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 29: 1 ORF40 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 30: 1 ORF42 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 31: 1 ORF43 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 32: 1 ORF44 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 33: 1 ORF46 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 34: 1 ORF49 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 35: 1 ORF50 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 36: 1 ORF51 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 37: 1 ORF58 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 38: 1 ORF61 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 39: 1 ORF62 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 40: 1 ORF64_1 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 41: 1 ORF66_1 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 42: 1 ORF68 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 43: 1 ORF73 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 44: 1 ORF74 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 45: 1 ORF75 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 46: 1 ORF76 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 47: 2 ORF5 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 48: 2 ORF7 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 49: 2 ORF10 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 50: 2 ORF17 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 51: 2 ORF30 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 52: 2 ORF53 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 53: 2 ORF63 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 54: 2 NOIR_2 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 55: 3 ORF6 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 56: 3 ORF65_1 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 57: 3 ORF67_1 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 58: 4 ORF12 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 59: 4 ORF13 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 60: 4 ORF15 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 61: 4 ORF16 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 62: 4 ORF27 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 63: 4 ORF32 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 64: 4 ORF35 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 65: 4 ORF41 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 66: 4 ORF48 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 67: 4 ORF52 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 68: 4 ORF54 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 69: 4 ORF57 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 70: 4 ORF59 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 71: 4 ORF60 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 72: 4 NOIR_1 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 73: 4 ORF71 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 74: 4 ORF72 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 75: 5 ORF69 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 76: 5 ORF70 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002481481 -2.6753919 0.9673845 0.46125656
## 2: 0.002481481 -2.6753919 0.9673845 0.46125656
## 3: 0.002481481 -2.6753919 0.9673845 0.46125656
## 4: 0.002481481 -2.6753919 0.9673845 0.46125656
## 5: 0.002481481 -2.6753919 0.9673845 0.46125656
## 6: 0.002481481 -2.6753919 0.9673845 0.46125656
## 7: 0.002481481 -2.6753919 0.9673845 0.46125656
## 8: 0.002481481 -2.6753919 0.9673845 0.46125656
## 9: 0.002481481 -2.6753919 0.9673845 0.46125656
## 10: 0.002481481 -2.6753919 0.9673845 0.46125656
## 11: 0.002481481 -2.6753919 0.9673845 0.46125656
## 12: 0.002481481 -2.6753919 0.9673845 0.46125656
## 13: 0.002481481 -2.6753919 0.9673845 0.46125656
## 14: 0.002481481 -2.6753919 0.9673845 0.46125656
## 15: 0.002481481 -2.6753919 0.9673845 0.46125656
## 16: 0.002481481 -2.6753919 0.9673845 0.46125656
## 17: 0.002481481 -2.6753919 0.9673845 0.46125656
## 18: 0.002481481 -2.6753919 0.9673845 0.46125656
## 19: 0.002481481 -2.6753919 0.9673845 0.46125656
## 20: 0.002481481 -2.6753919 0.9673845 0.46125656
## 21: 0.002481481 -2.6753919 0.9673845 0.46125656
## 22: 0.002481481 -2.6753919 0.9673845 0.46125656
## 23: 0.002481481 -2.6753919 0.9673845 0.46125656
## 24: 0.002481481 -2.6753919 0.9673845 0.46125656
## 25: 0.002481481 -2.6753919 0.9673845 0.46125656
## 26: 0.002481481 -2.6753919 0.9673845 0.46125656
## 27: 0.002481481 -2.6753919 0.9673845 0.46125656
## 28: 0.002481481 -2.6753919 0.9673845 0.46125656
## 29: 0.002481481 -2.6753919 0.9673845 0.46125656
## 30: 0.002481481 -2.6753919 0.9673845 0.46125656
## 31: 0.002481481 -2.6753919 0.9673845 0.46125656
## 32: 0.002481481 -2.6753919 0.9673845 0.46125656
## 33: 0.002481481 -2.6753919 0.9673845 0.46125656
## 34: 0.002481481 -2.6753919 0.9673845 0.46125656
## 35: 0.002481481 -2.6753919 0.9673845 0.46125656
## 36: 0.002481481 -2.6753919 0.9673845 0.46125656
## 37: 0.002481481 -2.6753919 0.9673845 0.46125656
## 38: 0.002481481 -2.6753919 0.9673845 0.46125656
## 39: 0.002481481 -2.6753919 0.9673845 0.46125656
## 40: 0.002481481 -2.6753919 0.9673845 0.46125656
## 41: 0.002481481 -2.6753919 0.9673845 0.46125656
## 42: 0.002481481 -2.6753919 0.9673845 0.46125656
## 43: 0.002481481 -2.6753919 0.9673845 0.46125656
## 44: 0.002481481 -2.6753919 0.9673845 0.46125656
## 45: 0.002481481 -2.6753919 0.9673845 0.46125656
## 46: 0.002481481 -2.6753919 0.9673845 0.46125656
## 47: 0.004817315 -1.4580182 0.8359843 0.01347018
## 48: 0.004817315 -1.4580182 0.8359843 0.01347018
## 49: 0.004817315 -1.4580182 0.8359843 0.01347018
## 50: 0.004817315 -1.4580182 0.8359843 0.01347018
## 51: 0.004817315 -1.4580182 0.8359843 0.01347018
## 52: 0.004817315 -1.4580182 0.8359843 0.01347018
## 53: 0.004817315 -1.4580182 0.8359843 0.01347018
## 54: 0.004817315 -1.4580182 0.8359843 0.01347018
## 55: 0.003763248 -2.3562552 1.1731165 0.10627673
## 56: 0.003763248 -2.3562552 1.1731165 0.10627673
## 57: 0.003763248 -2.3562552 1.1731165 0.10627673
## 58: 0.004507343 -1.6045906 0.8029487 0.17257690
## 59: 0.004507343 -1.6045906 0.8029487 0.17257690
## 60: 0.004507343 -1.6045906 0.8029487 0.17257690
## 61: 0.004507343 -1.6045906 0.8029487 0.17257690
## 62: 0.004507343 -1.6045906 0.8029487 0.17257690
## 63: 0.004507343 -1.6045906 0.8029487 0.17257690
## 64: 0.004507343 -1.6045906 0.8029487 0.17257690
## 65: 0.004507343 -1.6045906 0.8029487 0.17257690
## 66: 0.004507343 -1.6045906 0.8029487 0.17257690
## 67: 0.004507343 -1.6045906 0.8029487 0.17257690
## 68: 0.004507343 -1.6045906 0.8029487 0.17257690
## 69: 0.004507343 -1.6045906 0.8029487 0.17257690
## 70: 0.004507343 -1.6045906 0.8029487 0.17257690
## 71: 0.004507343 -1.6045906 0.8029487 0.17257690
## 72: 0.004507343 -1.6045906 0.8029487 0.17257690
## 73: 0.004507343 -1.6045906 0.8029487 0.17257690
## 74: 0.004507343 -1.6045906 0.8029487 0.17257690
## 75: 0.005060650 -0.7884213 0.3879516 0.10865152
## 76: 0.005060650 -0.7884213 0.3879516 0.10865152
## se.bp v c pchi
## [1] "ORF44" "ORF58" "ORF25" "ORF35.5" "ORF64_1" "ORF50" "ORF42"
## [8] "ORF33" "ORF34" "ORF62" "ORF4" "ORF20" "ORF21" "ORF61"
## [15] "ORF31" "ORF1" "NOIR_1" "ORF32" "ORF59" "ORF69"## [1] 20## [1] "ORF69" "ORF70"## [1] 2Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 2: 1 ORF4 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 3: 1 ORF9 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 4: 1 ORF19 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 5: 1 ORF20 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 6: 1 ORF21 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 7: 1 ORF31 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 8: 1 ORF34 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 9: 1 ORF37 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 10: 1 ORF38 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 11: 1 ORF49 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 12: 1 ORF50 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 13: 1 ORF51 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 14: 1 ORF61 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 15: 1 ORF64_1 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 16: 2 ORF2 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 17: 2 ORF3 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 18: 2 ORF8 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 19: 2 ORF11 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 20: 2 ORF14 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 21: 2 ORF18 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 22: 2 ORF22 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 23: 2 ORF23 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 24: 2 ORF24 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 25: 2 ORF25 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 26: 2 ORF26 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 27: 2 ORF28 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 28: 2 ORF29 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 29: 2 ORF33 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 30: 2 ORF35.5 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 31: 2 ORF36 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 32: 2 ORF39 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 33: 2 CTO 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 34: 2 ORF40 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 35: 2 ORF42 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 36: 2 ORF43 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 37: 2 ORF44 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 38: 2 ORF46 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 39: 2 ORF58 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 40: 2 ORF62 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 41: 2 ORF66_1 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 42: 2 ORF68 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 43: 2 ORF73 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 44: 2 ORF74 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 45: 2 ORF75 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 46: 2 ORF76 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 47: 3 ORF5 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 48: 3 ORF7 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 49: 3 ORF10 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 50: 3 ORF17 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 51: 3 ORF30 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 52: 3 ORF53 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 53: 3 ORF63 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 54: 3 NOIR_2 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 55: 4 ORF6 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 56: 4 ORF65_1 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 57: 4 ORF67_1 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 58: 5 ORF12 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 59: 5 ORF13 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 60: 5 ORF15 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 61: 5 ORF16 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 62: 5 ORF27 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 63: 5 ORF32 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 64: 5 ORF35 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 65: 5 ORF41 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 66: 5 ORF48 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 67: 5 ORF52 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 68: 5 ORF54 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 69: 5 ORF57 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 70: 5 ORF59 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 71: 5 ORF60 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 72: 5 NOIR_1 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 73: 5 ORF71 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 74: 5 ORF72 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 75: 6 ORF69 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 76: 6 ORF70 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002481481 -2.6753919 0.9673845 0.46125656
## 2: 0.002481481 -2.6753919 0.9673845 0.46125656
## 3: 0.002481481 -2.6753919 0.9673845 0.46125656
## 4: 0.002481481 -2.6753919 0.9673845 0.46125656
## 5: 0.002481481 -2.6753919 0.9673845 0.46125656
## 6: 0.002481481 -2.6753919 0.9673845 0.46125656
## 7: 0.002481481 -2.6753919 0.9673845 0.46125656
## 8: 0.002481481 -2.6753919 0.9673845 0.46125656
## 9: 0.002481481 -2.6753919 0.9673845 0.46125656
## 10: 0.002481481 -2.6753919 0.9673845 0.46125656
## 11: 0.002481481 -2.6753919 0.9673845 0.46125656
## 12: 0.002481481 -2.6753919 0.9673845 0.46125656
## 13: 0.002481481 -2.6753919 0.9673845 0.46125656
## 14: 0.002481481 -2.6753919 0.9673845 0.46125656
## 15: 0.002481481 -2.6753919 0.9673845 0.46125656
## 16: 0.004817315 -1.4580182 0.8359843 0.01347018
## 17: 0.004817315 -1.4580182 0.8359843 0.01347018
## 18: 0.004817315 -1.4580182 0.8359843 0.01347018
## 19: 0.004817315 -1.4580182 0.8359843 0.01347018
## 20: 0.004817315 -1.4580182 0.8359843 0.01347018
## 21: 0.004817315 -1.4580182 0.8359843 0.01347018
## 22: 0.004817315 -1.4580182 0.8359843 0.01347018
## 23: 0.004817315 -1.4580182 0.8359843 0.01347018
## 24: 0.004817315 -1.4580182 0.8359843 0.01347018
## 25: 0.004817315 -1.4580182 0.8359843 0.01347018
## 26: 0.004817315 -1.4580182 0.8359843 0.01347018
## 27: 0.004817315 -1.4580182 0.8359843 0.01347018
## 28: 0.004817315 -1.4580182 0.8359843 0.01347018
## 29: 0.004817315 -1.4580182 0.8359843 0.01347018
## 30: 0.004817315 -1.4580182 0.8359843 0.01347018
## 31: 0.004817315 -1.4580182 0.8359843 0.01347018
## 32: 0.004817315 -1.4580182 0.8359843 0.01347018
## 33: 0.004817315 -1.4580182 0.8359843 0.01347018
## 34: 0.004817315 -1.4580182 0.8359843 0.01347018
## 35: 0.004817315 -1.4580182 0.8359843 0.01347018
## 36: 0.004817315 -1.4580182 0.8359843 0.01347018
## 37: 0.004817315 -1.4580182 0.8359843 0.01347018
## 38: 0.004817315 -1.4580182 0.8359843 0.01347018
## 39: 0.004817315 -1.4580182 0.8359843 0.01347018
## 40: 0.004817315 -1.4580182 0.8359843 0.01347018
## 41: 0.004817315 -1.4580182 0.8359843 0.01347018
## 42: 0.004817315 -1.4580182 0.8359843 0.01347018
## 43: 0.004817315 -1.4580182 0.8359843 0.01347018
## 44: 0.004817315 -1.4580182 0.8359843 0.01347018
## 45: 0.004817315 -1.4580182 0.8359843 0.01347018
## 46: 0.004817315 -1.4580182 0.8359843 0.01347018
## 47: 0.003763248 -2.3562552 1.1731165 0.10627673
## 48: 0.003763248 -2.3562552 1.1731165 0.10627673
## 49: 0.003763248 -2.3562552 1.1731165 0.10627673
## 50: 0.003763248 -2.3562552 1.1731165 0.10627673
## 51: 0.003763248 -2.3562552 1.1731165 0.10627673
## 52: 0.003763248 -2.3562552 1.1731165 0.10627673
## 53: 0.003763248 -2.3562552 1.1731165 0.10627673
## 54: 0.003763248 -2.3562552 1.1731165 0.10627673
## 55: 0.004507343 -1.6045906 0.8029487 0.17257690
## 56: 0.004507343 -1.6045906 0.8029487 0.17257690
## 57: 0.004507343 -1.6045906 0.8029487 0.17257690
## 58: 0.005060650 -0.7884213 0.3879516 0.10865152
## 59: 0.005060650 -0.7884213 0.3879516 0.10865152
## 60: 0.005060650 -0.7884213 0.3879516 0.10865152
## 61: 0.005060650 -0.7884213 0.3879516 0.10865152
## 62: 0.005060650 -0.7884213 0.3879516 0.10865152
## 63: 0.005060650 -0.7884213 0.3879516 0.10865152
## 64: 0.005060650 -0.7884213 0.3879516 0.10865152
## 65: 0.005060650 -0.7884213 0.3879516 0.10865152
## 66: 0.005060650 -0.7884213 0.3879516 0.10865152
## 67: 0.005060650 -0.7884213 0.3879516 0.10865152
## 68: 0.005060650 -0.7884213 0.3879516 0.10865152
## 69: 0.005060650 -0.7884213 0.3879516 0.10865152
## 70: 0.005060650 -0.7884213 0.3879516 0.10865152
## 71: 0.005060650 -0.7884213 0.3879516 0.10865152
## 72: 0.005060650 -0.7884213 0.3879516 0.10865152
## 73: 0.005060650 -0.7884213 0.3879516 0.10865152
## 74: 0.005060650 -0.7884213 0.3879516 0.10865152
## 75: 0.005360343 -1.2234427 1.2472402 0.25815537
## 76: 0.005360343 -1.2234427 1.2472402 0.25815537
## se.bp v c pchi
## [1] "ORF61" "ORF21" "ORF49" "ORF19" "ORF31" "ORF1" "ORF62" "ORF18"
## [9] "ORF32" "ORF59" "NOIR_1" "ORF69"## [1] 12## [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF27" "ORF32" "ORF35" "ORF41"
## [9] "ORF48" "ORF52" "ORF54" "ORF57" "ORF59" "ORF60" "NOIR_1" "ORF71"
## [17] "ORF72"## [1] 17Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 2: 1 ORF4 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 3: 1 ORF9 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 4: 1 ORF19 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 5: 1 ORF20 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 6: 1 ORF21 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 7: 1 ORF31 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 8: 1 ORF34 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 9: 1 ORF37 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 10: 1 ORF38 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 11: 1 ORF49 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 12: 1 ORF50 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 13: 1 ORF51 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 14: 1 ORF61 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 15: 1 ORF64_1 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 16: 2 ORF2 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 17: 2 ORF3 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 18: 2 ORF8 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 19: 2 ORF11 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 20: 2 ORF14 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 21: 2 ORF18 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 22: 2 ORF22 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 23: 2 ORF23 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 24: 2 ORF24 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 25: 2 ORF25 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 26: 2 ORF26 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 27: 2 ORF28 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 28: 2 ORF29 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 29: 2 ORF33 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 30: 2 ORF35.5 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 31: 2 ORF36 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 32: 2 ORF39 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 33: 2 CTO 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 34: 2 ORF40 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 35: 2 ORF42 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 36: 2 ORF43 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 37: 2 ORF44 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 38: 2 ORF46 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 39: 2 ORF58 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 40: 2 ORF62 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 41: 2 ORF66_1 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 42: 2 ORF68 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 43: 2 ORF73 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 44: 2 ORF74 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 45: 2 ORF75 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 46: 2 ORF76 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 47: 3 ORF5 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 48: 3 ORF7 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 49: 3 ORF10 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 50: 3 ORF17 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 51: 3 ORF30 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 52: 3 ORF53 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 53: 3 ORF63 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 54: 3 NOIR_2 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 55: 4 ORF6 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 56: 4 ORF65_1 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 57: 4 ORF67_1 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 58: 5 ORF12 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 59: 5 ORF13 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 60: 5 ORF15 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 61: 5 ORF16 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 62: 5 ORF35 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 63: 5 ORF41 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 64: 5 ORF48 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 65: 5 ORF52 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 66: 5 ORF54 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 67: 5 ORF57 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 68: 5 ORF60 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 69: 5 ORF71 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 70: 5 ORF72 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 71: 6 ORF27 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 72: 6 ORF32 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 73: 6 ORF59 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 74: 6 NOIR_1 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 75: 7 ORF69 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 76: 7 ORF70 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002481481 -2.6753919 0.9673845 0.46125656
## 2: 0.002481481 -2.6753919 0.9673845 0.46125656
## 3: 0.002481481 -2.6753919 0.9673845 0.46125656
## 4: 0.002481481 -2.6753919 0.9673845 0.46125656
## 5: 0.002481481 -2.6753919 0.9673845 0.46125656
## 6: 0.002481481 -2.6753919 0.9673845 0.46125656
## 7: 0.002481481 -2.6753919 0.9673845 0.46125656
## 8: 0.002481481 -2.6753919 0.9673845 0.46125656
## 9: 0.002481481 -2.6753919 0.9673845 0.46125656
## 10: 0.002481481 -2.6753919 0.9673845 0.46125656
## 11: 0.002481481 -2.6753919 0.9673845 0.46125656
## 12: 0.002481481 -2.6753919 0.9673845 0.46125656
## 13: 0.002481481 -2.6753919 0.9673845 0.46125656
## 14: 0.002481481 -2.6753919 0.9673845 0.46125656
## 15: 0.002481481 -2.6753919 0.9673845 0.46125656
## 16: 0.004817315 -1.4580182 0.8359843 0.01347018
## 17: 0.004817315 -1.4580182 0.8359843 0.01347018
## 18: 0.004817315 -1.4580182 0.8359843 0.01347018
## 19: 0.004817315 -1.4580182 0.8359843 0.01347018
## 20: 0.004817315 -1.4580182 0.8359843 0.01347018
## 21: 0.004817315 -1.4580182 0.8359843 0.01347018
## 22: 0.004817315 -1.4580182 0.8359843 0.01347018
## 23: 0.004817315 -1.4580182 0.8359843 0.01347018
## 24: 0.004817315 -1.4580182 0.8359843 0.01347018
## 25: 0.004817315 -1.4580182 0.8359843 0.01347018
## 26: 0.004817315 -1.4580182 0.8359843 0.01347018
## 27: 0.004817315 -1.4580182 0.8359843 0.01347018
## 28: 0.004817315 -1.4580182 0.8359843 0.01347018
## 29: 0.004817315 -1.4580182 0.8359843 0.01347018
## 30: 0.004817315 -1.4580182 0.8359843 0.01347018
## 31: 0.004817315 -1.4580182 0.8359843 0.01347018
## 32: 0.004817315 -1.4580182 0.8359843 0.01347018
## 33: 0.004817315 -1.4580182 0.8359843 0.01347018
## 34: 0.004817315 -1.4580182 0.8359843 0.01347018
## 35: 0.004817315 -1.4580182 0.8359843 0.01347018
## 36: 0.004817315 -1.4580182 0.8359843 0.01347018
## 37: 0.004817315 -1.4580182 0.8359843 0.01347018
## 38: 0.004817315 -1.4580182 0.8359843 0.01347018
## 39: 0.004817315 -1.4580182 0.8359843 0.01347018
## 40: 0.004817315 -1.4580182 0.8359843 0.01347018
## 41: 0.004817315 -1.4580182 0.8359843 0.01347018
## 42: 0.004817315 -1.4580182 0.8359843 0.01347018
## 43: 0.004817315 -1.4580182 0.8359843 0.01347018
## 44: 0.004817315 -1.4580182 0.8359843 0.01347018
## 45: 0.004817315 -1.4580182 0.8359843 0.01347018
## 46: 0.004817315 -1.4580182 0.8359843 0.01347018
## 47: 0.003763248 -2.3562552 1.1731165 0.10627673
## 48: 0.003763248 -2.3562552 1.1731165 0.10627673
## 49: 0.003763248 -2.3562552 1.1731165 0.10627673
## 50: 0.003763248 -2.3562552 1.1731165 0.10627673
## 51: 0.003763248 -2.3562552 1.1731165 0.10627673
## 52: 0.003763248 -2.3562552 1.1731165 0.10627673
## 53: 0.003763248 -2.3562552 1.1731165 0.10627673
## 54: 0.003763248 -2.3562552 1.1731165 0.10627673
## 55: 0.004507343 -1.6045906 0.8029487 0.17257690
## 56: 0.004507343 -1.6045906 0.8029487 0.17257690
## 57: 0.004507343 -1.6045906 0.8029487 0.17257690
## 58: 0.005060650 -0.7884213 0.3879516 0.10865152
## 59: 0.005060650 -0.7884213 0.3879516 0.10865152
## 60: 0.005060650 -0.7884213 0.3879516 0.10865152
## 61: 0.005060650 -0.7884213 0.3879516 0.10865152
## 62: 0.005060650 -0.7884213 0.3879516 0.10865152
## 63: 0.005060650 -0.7884213 0.3879516 0.10865152
## 64: 0.005060650 -0.7884213 0.3879516 0.10865152
## 65: 0.005060650 -0.7884213 0.3879516 0.10865152
## 66: 0.005060650 -0.7884213 0.3879516 0.10865152
## 67: 0.005060650 -0.7884213 0.3879516 0.10865152
## 68: 0.005060650 -0.7884213 0.3879516 0.10865152
## 69: 0.005060650 -0.7884213 0.3879516 0.10865152
## 70: 0.005060650 -0.7884213 0.3879516 0.10865152
## 71: 0.005360343 -1.2234427 1.2472402 0.25815537
## 72: 0.005360343 -1.2234427 1.2472402 0.25815537
## 73: 0.005360343 -1.2234427 1.2472402 0.25815537
## 74: 0.005360343 -1.2234427 1.2472402 0.25815537
## 75: 0.004386235 -2.0285561 1.1189850 0.70546926
## 76: 0.004386235 -2.0285561 1.1189850 0.70546926
## se.bp v c pchi
## [1] "ORF61" "ORF21" "ORF49" "ORF19" "ORF31" "ORF1" "ORF18" "ORF42" "ORF33"
## [10] "ORF62" "ORF69"## [1] 11## [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF48" "ORF52" "ORF54"
## [10] "ORF57" "ORF60" "ORF71" "ORF72"## [1] 13Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 2: 1 ORF4 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 3: 1 ORF9 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 4: 1 ORF20 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 5: 1 ORF21 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 6: 1 ORF31 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 7: 1 ORF34 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 8: 1 ORF38 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 9: 1 ORF50 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 10: 1 ORF61 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 11: 1 ORF64_1 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 12: 2 ORF2 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 13: 2 ORF3 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 14: 2 ORF11 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 15: 2 ORF14 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 16: 2 ORF18 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 17: 2 ORF26 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 18: 2 ORF28 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 19: 2 ORF29 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 20: 2 ORF39 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 21: 2 ORF40 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 22: 2 ORF66_1 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 23: 2 ORF68 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 24: 2 ORF73 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 25: 2 ORF75 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 26: 2 ORF76 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 27: 3 ORF5 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 28: 3 ORF7 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 29: 3 ORF10 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 30: 3 ORF17 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 31: 3 ORF30 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 32: 3 ORF53 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 33: 3 ORF63 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 34: 3 NOIR_2 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 35: 4 ORF6 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 36: 4 ORF65_1 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 37: 4 ORF67_1 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 38: 5 ORF8 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 39: 5 ORF22 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 40: 5 ORF23 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 41: 5 ORF25 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 42: 5 ORF33 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 43: 5 ORF35.5 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 44: 5 ORF36 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 45: 5 CTO 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 46: 5 ORF42 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 47: 5 ORF43 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 48: 5 ORF44 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 49: 5 ORF46 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 50: 5 ORF58 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 51: 5 ORF62 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 52: 6 ORF12 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 53: 6 ORF13 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 54: 6 ORF15 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 55: 6 ORF16 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 56: 6 ORF35 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 57: 6 ORF41 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 58: 6 ORF48 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 59: 6 ORF52 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 60: 6 ORF54 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 61: 6 ORF57 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 62: 6 ORF60 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 63: 6 ORF71 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 64: 6 ORF72 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 65: 7 ORF19 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 66: 7 ORF37 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 67: 7 ORF49 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 68: 7 ORF51 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 69: 8 ORF24 0.8474370 0.9660387 0.6174048 0.0192056101 5.939429e-03
## 70: 8 ORF74 0.8474370 0.9660387 0.6174048 0.0192056101 5.939429e-03
## 71: 9 ORF27 0.4076975 0.8590551 0.3632933 0.0467484779 1.809760e-02
## 72: 9 ORF32 0.4076975 0.8590551 0.3632933 0.0467484779 1.809760e-02
## 73: 9 ORF59 0.4076975 0.8590551 0.3632933 0.0467484779 1.809760e-02
## 74: 9 NOIR_1 0.4076975 0.8590551 0.3632933 0.0467484779 1.809760e-02
## 75: 10 ORF69 0.9896091 0.9987380 0.7533165 0.0022422376 3.532349e-04
## 76: 10 ORF70 0.9896091 0.9987380 0.7533165 0.0022422376 3.532349e-04
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002481481 -2.6753919 0.9673845 0.46125656
## 2: 0.002481481 -2.6753919 0.9673845 0.46125656
## 3: 0.002481481 -2.6753919 0.9673845 0.46125656
## 4: 0.002481481 -2.6753919 0.9673845 0.46125656
## 5: 0.002481481 -2.6753919 0.9673845 0.46125656
## 6: 0.002481481 -2.6753919 0.9673845 0.46125656
## 7: 0.002481481 -2.6753919 0.9673845 0.46125656
## 8: 0.002481481 -2.6753919 0.9673845 0.46125656
## 9: 0.002481481 -2.6753919 0.9673845 0.46125656
## 10: 0.002481481 -2.6753919 0.9673845 0.46125656
## 11: 0.002481481 -2.6753919 0.9673845 0.46125656
## 12: 0.004817315 -1.4580182 0.8359843 0.01347018
## 13: 0.004817315 -1.4580182 0.8359843 0.01347018
## 14: 0.004817315 -1.4580182 0.8359843 0.01347018
## 15: 0.004817315 -1.4580182 0.8359843 0.01347018
## 16: 0.004817315 -1.4580182 0.8359843 0.01347018
## 17: 0.004817315 -1.4580182 0.8359843 0.01347018
## 18: 0.004817315 -1.4580182 0.8359843 0.01347018
## 19: 0.004817315 -1.4580182 0.8359843 0.01347018
## 20: 0.004817315 -1.4580182 0.8359843 0.01347018
## 21: 0.004817315 -1.4580182 0.8359843 0.01347018
## 22: 0.004817315 -1.4580182 0.8359843 0.01347018
## 23: 0.004817315 -1.4580182 0.8359843 0.01347018
## 24: 0.004817315 -1.4580182 0.8359843 0.01347018
## 25: 0.004817315 -1.4580182 0.8359843 0.01347018
## 26: 0.004817315 -1.4580182 0.8359843 0.01347018
## 27: 0.003763248 -2.3562552 1.1731165 0.10627673
## 28: 0.003763248 -2.3562552 1.1731165 0.10627673
## 29: 0.003763248 -2.3562552 1.1731165 0.10627673
## 30: 0.003763248 -2.3562552 1.1731165 0.10627673
## 31: 0.003763248 -2.3562552 1.1731165 0.10627673
## 32: 0.003763248 -2.3562552 1.1731165 0.10627673
## 33: 0.003763248 -2.3562552 1.1731165 0.10627673
## 34: 0.003763248 -2.3562552 1.1731165 0.10627673
## 35: 0.004507343 -1.6045906 0.8029487 0.17257690
## 36: 0.004507343 -1.6045906 0.8029487 0.17257690
## 37: 0.004507343 -1.6045906 0.8029487 0.17257690
## 38: 0.005060650 -0.7884213 0.3879516 0.10865152
## 39: 0.005060650 -0.7884213 0.3879516 0.10865152
## 40: 0.005060650 -0.7884213 0.3879516 0.10865152
## 41: 0.005060650 -0.7884213 0.3879516 0.10865152
## 42: 0.005060650 -0.7884213 0.3879516 0.10865152
## 43: 0.005060650 -0.7884213 0.3879516 0.10865152
## 44: 0.005060650 -0.7884213 0.3879516 0.10865152
## 45: 0.005060650 -0.7884213 0.3879516 0.10865152
## 46: 0.005060650 -0.7884213 0.3879516 0.10865152
## 47: 0.005060650 -0.7884213 0.3879516 0.10865152
## 48: 0.005060650 -0.7884213 0.3879516 0.10865152
## 49: 0.005060650 -0.7884213 0.3879516 0.10865152
## 50: 0.005060650 -0.7884213 0.3879516 0.10865152
## 51: 0.005060650 -0.7884213 0.3879516 0.10865152
## 52: 0.005360343 -1.2234427 1.2472402 0.25815537
## 53: 0.005360343 -1.2234427 1.2472402 0.25815537
## 54: 0.005360343 -1.2234427 1.2472402 0.25815537
## 55: 0.005360343 -1.2234427 1.2472402 0.25815537
## 56: 0.005360343 -1.2234427 1.2472402 0.25815537
## 57: 0.005360343 -1.2234427 1.2472402 0.25815537
## 58: 0.005360343 -1.2234427 1.2472402 0.25815537
## 59: 0.005360343 -1.2234427 1.2472402 0.25815537
## 60: 0.005360343 -1.2234427 1.2472402 0.25815537
## 61: 0.005360343 -1.2234427 1.2472402 0.25815537
## 62: 0.005360343 -1.2234427 1.2472402 0.25815537
## 63: 0.005360343 -1.2234427 1.2472402 0.25815537
## 64: 0.005360343 -1.2234427 1.2472402 0.25815537
## 65: 0.004386235 -2.0285561 1.1189850 0.70546926
## 66: 0.004386235 -2.0285561 1.1189850 0.70546926
## 67: 0.004386235 -2.0285561 1.1189850 0.70546926
## 68: 0.004386235 -2.0285561 1.1189850 0.70546926
## 69: 0.005208593 -1.0620956 0.7634238 0.08979962
## 70: 0.005208593 -1.0620956 0.7634238 0.08979962
## 71: 0.005063398 -0.3632070 0.7128767 0.22196887
## 72: 0.005063398 -0.3632070 0.7128767 0.22196887
## 73: 0.005063398 -0.3632070 0.7128767 0.22196887
## 74: 0.005063398 -0.3632070 0.7128767 0.22196887
## 75: 0.004813843 -1.8527010 1.1677376 0.91850610
## 76: 0.004813843 -1.8527010 1.1677376 0.91850610
## se.bp v c pchi
## [1] "ORF1" "ORF68" "ORF36" "ORF19" "ORF49" "ORF59" "ORF69"## [1] 7## [1] "ORF8" "ORF22" "ORF23" "ORF25" "ORF33" "ORF35.5" "ORF36"
## [8] "CTO" "ORF42" "ORF43" "ORF44" "ORF46" "ORF58" "ORF62"
## [15] "ORF27" "ORF32" "ORF59" "NOIR_1"## [1] 18Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 2: 1 ORF4 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 3: 1 ORF9 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 4: 1 ORF20 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 5: 1 ORF21 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 6: 1 ORF31 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 7: 1 ORF34 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 8: 1 ORF38 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 9: 1 ORF50 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 10: 1 ORF61 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 11: 2 ORF2 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 12: 2 ORF3 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 13: 2 ORF11 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 14: 2 ORF14 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 15: 2 ORF18 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 16: 2 ORF26 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 17: 2 ORF28 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 18: 2 ORF29 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 19: 2 ORF39 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 20: 2 ORF40 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 21: 2 ORF66_1 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 22: 2 ORF68 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 23: 2 ORF73 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 24: 2 ORF75 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 25: 2 ORF76 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 26: 3 ORF5 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 27: 3 ORF7 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 28: 3 ORF10 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 29: 3 ORF17 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 30: 3 ORF30 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 31: 3 ORF53 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 32: 3 ORF63 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 33: 3 NOIR_2 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 34: 4 ORF6 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 35: 4 ORF65_1 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 36: 4 ORF67_1 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 37: 5 ORF8 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 38: 5 ORF22 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 39: 5 ORF23 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 40: 5 ORF25 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 41: 5 ORF33 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 42: 5 ORF35.5 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 43: 5 ORF36 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 44: 5 CTO 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 45: 5 ORF42 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 46: 5 ORF43 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 47: 5 ORF44 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 48: 5 ORF46 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 49: 5 ORF58 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 50: 5 ORF62 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 51: 6 ORF12 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 52: 6 ORF13 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 53: 6 ORF15 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 54: 6 ORF16 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 55: 6 ORF35 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 56: 6 ORF41 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 57: 6 ORF48 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 58: 6 ORF52 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 59: 6 ORF54 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 60: 6 ORF57 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 61: 6 ORF60 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 62: 6 ORF71 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 63: 6 ORF72 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 64: 7 ORF19 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 65: 7 ORF37 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 66: 7 ORF49 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 67: 7 ORF51 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 68: 8 ORF24 0.8474370 0.9660387 0.6174048 0.0192056101 5.939429e-03
## 69: 8 ORF74 0.8474370 0.9660387 0.6174048 0.0192056101 5.939429e-03
## 70: 9 ORF27 0.4076975 0.8590551 0.3632933 0.0467484779 1.809760e-02
## 71: 9 ORF32 0.4076975 0.8590551 0.3632933 0.0467484779 1.809760e-02
## 72: 9 ORF59 0.4076975 0.8590551 0.3632933 0.0467484779 1.809760e-02
## 73: 10 ORF64_1 0.9896091 0.9987380 0.7533165 0.0022422376 3.532349e-04
## 74: 11 NOIR_1 0.9913633 0.9988278 0.8004577 0.0019533968 3.389403e-04
## 75: 12 ORF69 0.6115997 0.9462193 0.2859647 0.0434095595 9.613566e-03
## 76: 12 ORF70 0.6115997 0.9462193 0.2859647 0.0434095595 9.613566e-03
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002481481 -2.6753919 0.9673845 0.46125656
## 2: 0.002481481 -2.6753919 0.9673845 0.46125656
## 3: 0.002481481 -2.6753919 0.9673845 0.46125656
## 4: 0.002481481 -2.6753919 0.9673845 0.46125656
## 5: 0.002481481 -2.6753919 0.9673845 0.46125656
## 6: 0.002481481 -2.6753919 0.9673845 0.46125656
## 7: 0.002481481 -2.6753919 0.9673845 0.46125656
## 8: 0.002481481 -2.6753919 0.9673845 0.46125656
## 9: 0.002481481 -2.6753919 0.9673845 0.46125656
## 10: 0.002481481 -2.6753919 0.9673845 0.46125656
## 11: 0.004817315 -1.4580182 0.8359843 0.01347018
## 12: 0.004817315 -1.4580182 0.8359843 0.01347018
## 13: 0.004817315 -1.4580182 0.8359843 0.01347018
## 14: 0.004817315 -1.4580182 0.8359843 0.01347018
## 15: 0.004817315 -1.4580182 0.8359843 0.01347018
## 16: 0.004817315 -1.4580182 0.8359843 0.01347018
## 17: 0.004817315 -1.4580182 0.8359843 0.01347018
## 18: 0.004817315 -1.4580182 0.8359843 0.01347018
## 19: 0.004817315 -1.4580182 0.8359843 0.01347018
## 20: 0.004817315 -1.4580182 0.8359843 0.01347018
## 21: 0.004817315 -1.4580182 0.8359843 0.01347018
## 22: 0.004817315 -1.4580182 0.8359843 0.01347018
## 23: 0.004817315 -1.4580182 0.8359843 0.01347018
## 24: 0.004817315 -1.4580182 0.8359843 0.01347018
## 25: 0.004817315 -1.4580182 0.8359843 0.01347018
## 26: 0.003763248 -2.3562552 1.1731165 0.10627673
## 27: 0.003763248 -2.3562552 1.1731165 0.10627673
## 28: 0.003763248 -2.3562552 1.1731165 0.10627673
## 29: 0.003763248 -2.3562552 1.1731165 0.10627673
## 30: 0.003763248 -2.3562552 1.1731165 0.10627673
## 31: 0.003763248 -2.3562552 1.1731165 0.10627673
## 32: 0.003763248 -2.3562552 1.1731165 0.10627673
## 33: 0.003763248 -2.3562552 1.1731165 0.10627673
## 34: 0.004507343 -1.6045906 0.8029487 0.17257690
## 35: 0.004507343 -1.6045906 0.8029487 0.17257690
## 36: 0.004507343 -1.6045906 0.8029487 0.17257690
## 37: 0.005060650 -0.7884213 0.3879516 0.10865152
## 38: 0.005060650 -0.7884213 0.3879516 0.10865152
## 39: 0.005060650 -0.7884213 0.3879516 0.10865152
## 40: 0.005060650 -0.7884213 0.3879516 0.10865152
## 41: 0.005060650 -0.7884213 0.3879516 0.10865152
## 42: 0.005060650 -0.7884213 0.3879516 0.10865152
## 43: 0.005060650 -0.7884213 0.3879516 0.10865152
## 44: 0.005060650 -0.7884213 0.3879516 0.10865152
## 45: 0.005060650 -0.7884213 0.3879516 0.10865152
## 46: 0.005060650 -0.7884213 0.3879516 0.10865152
## 47: 0.005060650 -0.7884213 0.3879516 0.10865152
## 48: 0.005060650 -0.7884213 0.3879516 0.10865152
## 49: 0.005060650 -0.7884213 0.3879516 0.10865152
## 50: 0.005060650 -0.7884213 0.3879516 0.10865152
## 51: 0.005360343 -1.2234427 1.2472402 0.25815537
## 52: 0.005360343 -1.2234427 1.2472402 0.25815537
## 53: 0.005360343 -1.2234427 1.2472402 0.25815537
## 54: 0.005360343 -1.2234427 1.2472402 0.25815537
## 55: 0.005360343 -1.2234427 1.2472402 0.25815537
## 56: 0.005360343 -1.2234427 1.2472402 0.25815537
## 57: 0.005360343 -1.2234427 1.2472402 0.25815537
## 58: 0.005360343 -1.2234427 1.2472402 0.25815537
## 59: 0.005360343 -1.2234427 1.2472402 0.25815537
## 60: 0.005360343 -1.2234427 1.2472402 0.25815537
## 61: 0.005360343 -1.2234427 1.2472402 0.25815537
## 62: 0.005360343 -1.2234427 1.2472402 0.25815537
## 63: 0.005360343 -1.2234427 1.2472402 0.25815537
## 64: 0.004386235 -2.0285561 1.1189850 0.70546926
## 65: 0.004386235 -2.0285561 1.1189850 0.70546926
## 66: 0.004386235 -2.0285561 1.1189850 0.70546926
## 67: 0.004386235 -2.0285561 1.1189850 0.70546926
## 68: 0.005208593 -1.0620956 0.7634238 0.08979962
## 69: 0.005208593 -1.0620956 0.7634238 0.08979962
## 70: 0.005063398 -0.3632070 0.7128767 0.22196887
## 71: 0.005063398 -0.3632070 0.7128767 0.22196887
## 72: 0.005063398 -0.3632070 0.7128767 0.22196887
## 73: 0.004813843 -1.8527010 1.1677376 0.91850610
## 74: 0.004502973 -1.9429961 1.0997388 0.53648615
## 75: 0.004750259 -0.5220195 1.0872318 0.89696383
## 76: 0.004750259 -0.5220195 1.0872318 0.89696383
## se.bp v c pchi
## [1] "ORF68" "ORF36" "ORF19" "ORF49" "ORF69"## [1] 5## [1] "ORF8" "ORF22" "ORF23" "ORF25" "ORF33" "ORF35.5" "ORF36"
## [8] "CTO" "ORF42" "ORF43" "ORF44" "ORF46" "ORF58" "ORF62"
## [15] "ORF27" "ORF32" "ORF59" "ORF69" "ORF70"## [1] 19Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 2: 1 ORF4 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 3: 1 ORF9 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 4: 1 ORF20 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 5: 1 ORF21 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 6: 1 ORF31 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 7: 1 ORF34 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 8: 1 ORF38 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 9: 1 ORF50 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 10: 1 ORF61 0.9991909 0.9998651 0.9561825 0.0003253987 6.473120e-05
## 11: 2 ORF2 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 12: 2 ORF3 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 13: 2 ORF11 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 14: 2 ORF14 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 15: 2 ORF18 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 16: 2 ORF26 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 17: 2 ORF28 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 18: 2 ORF29 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 19: 2 ORF39 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 20: 2 ORF40 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 21: 2 ORF66_1 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 22: 2 ORF68 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 23: 2 ORF73 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 24: 2 ORF75 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 25: 2 ORF76 0.9459516 0.9891048 0.7330402 0.0088116038 2.345669e-03
## 26: 3 ORF5 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 27: 3 ORF7 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 28: 3 ORF10 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 29: 3 ORF17 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 30: 3 ORF30 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 31: 3 ORF53 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 32: 3 ORF63 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 33: 3 NOIR_2 0.9982698 0.9997917 0.8816229 0.0005092158 7.599843e-05
## 34: 4 ORF6 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 35: 4 ORF65_1 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 36: 4 ORF67_1 0.9619425 0.9919698 0.7886199 0.0068313332 1.864515e-03
## 37: 5 ORF8 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 38: 5 ORF22 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 39: 5 ORF23 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 40: 5 ORF25 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 41: 5 ORF33 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 42: 5 ORF35.5 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 43: 5 ORF36 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 44: 5 CTO 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 45: 5 ORF42 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 46: 5 ORF43 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 47: 5 ORF44 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 48: 5 ORF46 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 49: 5 ORF58 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 50: 5 ORF62 0.6569798 0.8802770 0.6555947 0.0316295048 1.564437e-02
## 51: 6 ORF12 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 52: 6 ORF13 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 53: 6 ORF15 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 54: 6 ORF16 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 55: 6 ORF35 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 56: 6 ORF41 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 57: 6 ORF48 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 58: 6 ORF52 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 59: 6 ORF54 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 60: 6 ORF57 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 61: 6 ORF60 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 62: 6 ORF71 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 63: 6 ORF72 0.9364817 0.9932572 0.4905071 0.0103219970 1.546849e-03
## 64: 7 ORF19 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 65: 7 ORF37 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 66: 7 ORF49 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 67: 7 ORF51 0.9937430 0.9991768 0.8184756 0.0014993562 2.504902e-04
## 68: 8 ORF24 0.8474370 0.9660387 0.6174048 0.0192056101 5.939429e-03
## 69: 8 ORF74 0.8474370 0.9660387 0.6174048 0.0192056101 5.939429e-03
## 70: 9 ORF27 0.4076975 0.8590551 0.3632933 0.0467484779 1.809760e-02
## 71: 9 ORF32 0.4076975 0.8590551 0.3632933 0.0467484779 1.809760e-02
## 72: 9 ORF59 0.4076975 0.8590551 0.3632933 0.0467484779 1.809760e-02
## 73: 10 ORF64_1 0.9896091 0.9987380 0.7533165 0.0022422376 3.532349e-04
## 74: 11 NOIR_1 0.9913633 0.9988278 0.8004577 0.0019533968 3.389403e-04
## 75: 12 ORF69 0.6115997 0.9462193 0.2859647 0.0434095595 9.613566e-03
## 76: 12 ORF70 0.6115997 0.9462193 0.2859647 0.0434095595 9.613566e-03
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002481481 -2.6753919 0.9673845 0.46125656
## 2: 0.002481481 -2.6753919 0.9673845 0.46125656
## 3: 0.002481481 -2.6753919 0.9673845 0.46125656
## 4: 0.002481481 -2.6753919 0.9673845 0.46125656
## 5: 0.002481481 -2.6753919 0.9673845 0.46125656
## 6: 0.002481481 -2.6753919 0.9673845 0.46125656
## 7: 0.002481481 -2.6753919 0.9673845 0.46125656
## 8: 0.002481481 -2.6753919 0.9673845 0.46125656
## 9: 0.002481481 -2.6753919 0.9673845 0.46125656
## 10: 0.002481481 -2.6753919 0.9673845 0.46125656
## 11: 0.004817315 -1.4580182 0.8359843 0.01347018
## 12: 0.004817315 -1.4580182 0.8359843 0.01347018
## 13: 0.004817315 -1.4580182 0.8359843 0.01347018
## 14: 0.004817315 -1.4580182 0.8359843 0.01347018
## 15: 0.004817315 -1.4580182 0.8359843 0.01347018
## 16: 0.004817315 -1.4580182 0.8359843 0.01347018
## 17: 0.004817315 -1.4580182 0.8359843 0.01347018
## 18: 0.004817315 -1.4580182 0.8359843 0.01347018
## 19: 0.004817315 -1.4580182 0.8359843 0.01347018
## 20: 0.004817315 -1.4580182 0.8359843 0.01347018
## 21: 0.004817315 -1.4580182 0.8359843 0.01347018
## 22: 0.004817315 -1.4580182 0.8359843 0.01347018
## 23: 0.004817315 -1.4580182 0.8359843 0.01347018
## 24: 0.004817315 -1.4580182 0.8359843 0.01347018
## 25: 0.004817315 -1.4580182 0.8359843 0.01347018
## 26: 0.003763248 -2.3562552 1.1731165 0.10627673
## 27: 0.003763248 -2.3562552 1.1731165 0.10627673
## 28: 0.003763248 -2.3562552 1.1731165 0.10627673
## 29: 0.003763248 -2.3562552 1.1731165 0.10627673
## 30: 0.003763248 -2.3562552 1.1731165 0.10627673
## 31: 0.003763248 -2.3562552 1.1731165 0.10627673
## 32: 0.003763248 -2.3562552 1.1731165 0.10627673
## 33: 0.003763248 -2.3562552 1.1731165 0.10627673
## 34: 0.004507343 -1.6045906 0.8029487 0.17257690
## 35: 0.004507343 -1.6045906 0.8029487 0.17257690
## 36: 0.004507343 -1.6045906 0.8029487 0.17257690
## 37: 0.005060650 -0.7884213 0.3879516 0.10865152
## 38: 0.005060650 -0.7884213 0.3879516 0.10865152
## 39: 0.005060650 -0.7884213 0.3879516 0.10865152
## 40: 0.005060650 -0.7884213 0.3879516 0.10865152
## 41: 0.005060650 -0.7884213 0.3879516 0.10865152
## 42: 0.005060650 -0.7884213 0.3879516 0.10865152
## 43: 0.005060650 -0.7884213 0.3879516 0.10865152
## 44: 0.005060650 -0.7884213 0.3879516 0.10865152
## 45: 0.005060650 -0.7884213 0.3879516 0.10865152
## 46: 0.005060650 -0.7884213 0.3879516 0.10865152
## 47: 0.005060650 -0.7884213 0.3879516 0.10865152
## 48: 0.005060650 -0.7884213 0.3879516 0.10865152
## 49: 0.005060650 -0.7884213 0.3879516 0.10865152
## 50: 0.005060650 -0.7884213 0.3879516 0.10865152
## 51: 0.005360343 -1.2234427 1.2472402 0.25815537
## 52: 0.005360343 -1.2234427 1.2472402 0.25815537
## 53: 0.005360343 -1.2234427 1.2472402 0.25815537
## 54: 0.005360343 -1.2234427 1.2472402 0.25815537
## 55: 0.005360343 -1.2234427 1.2472402 0.25815537
## 56: 0.005360343 -1.2234427 1.2472402 0.25815537
## 57: 0.005360343 -1.2234427 1.2472402 0.25815537
## 58: 0.005360343 -1.2234427 1.2472402 0.25815537
## 59: 0.005360343 -1.2234427 1.2472402 0.25815537
## 60: 0.005360343 -1.2234427 1.2472402 0.25815537
## 61: 0.005360343 -1.2234427 1.2472402 0.25815537
## 62: 0.005360343 -1.2234427 1.2472402 0.25815537
## 63: 0.005360343 -1.2234427 1.2472402 0.25815537
## 64: 0.004386235 -2.0285561 1.1189850 0.70546926
## 65: 0.004386235 -2.0285561 1.1189850 0.70546926
## 66: 0.004386235 -2.0285561 1.1189850 0.70546926
## 67: 0.004386235 -2.0285561 1.1189850 0.70546926
## 68: 0.005208593 -1.0620956 0.7634238 0.08979962
## 69: 0.005208593 -1.0620956 0.7634238 0.08979962
## 70: 0.005063398 -0.3632070 0.7128767 0.22196887
## 71: 0.005063398 -0.3632070 0.7128767 0.22196887
## 72: 0.005063398 -0.3632070 0.7128767 0.22196887
## 73: 0.004813843 -1.8527010 1.1677376 0.91850610
## 74: 0.004502973 -1.9429961 1.0997388 0.53648615
## 75: 0.004750259 -0.5220195 1.0872318 0.89696383
## 76: 0.004750259 -0.5220195 1.0872318 0.89696383
## se.bp v c pchi
## [1] "ORF68" "ORF36" "ORF19" "ORF49" "ORF69"## [1] 5## [1] "ORF8" "ORF22" "ORF23" "ORF25" "ORF33" "ORF35.5" "ORF36"
## [8] "CTO" "ORF42" "ORF43" "ORF44" "ORF46" "ORF58" "ORF62"
## [15] "ORF27" "ORF32" "ORF59" "ORF69" "ORF70"## [1] 19Remove genes from clusters ?
## [1] "ORF8" "ORF22" "ORF23" "ORF25" "ORF33" "ORF35.5" "ORF36"
## [8] "CTO" "ORF42" "ORF43" "ORF44" "ORF46" "ORF58" "ORF62"
## [15] "ORF27" "ORF32" "ORF59" "ORF69" "ORF70"## [1] 19## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 2 15
## 2: 5 14
## 3: 6 13
## 4: 1 10
## 5: 3 8
## 6: 7 4
## 7: 4 3
## 8: 9 3
## 9: 8 2
## 10: 12 2
## 11: 10 1
## 12: 11 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
